Opal 4.15 Release Notes

Charlene Son-Rigby -

17 November 2015

Opal 4.15 is now live! 

We are excited to announce the release of VAAST 3. VAAST is already the industry-leading algorithm for ranking causative variants and genes, significantly accelerating diagnosis and disease gene discovery. We continue to innovate and drive forward technological advancement with our long-time collaborators at University of Utah. VAAST 3 delivers substantial improvements over VAAST 2, with increased speed, broader coverage and improved ranking results.

VAAST is incorporated into the standardized clinical interpretation workflows in Opal Clinical. Opal Clinical provides an end-to-end solution for clinical NGS testing, combining Omicia’s industry-leading Opal annotation platform with structured workflows, full support for clinical report generation, curated gene panels and LIS integration -- all within a secure, HIPAA-compliant environment. Contact sales@omicia.com if you’d like to try Opal Clinical.

 

VAAST 3

Reducing False Positives in Family Reports using Ref Call & No Call Data

Data Source & Algorithm Versions

 

VAAST 3

VAAST 3 delivers substantial improvements over VAAST 2, with increased speed, broader coverage and improved ranking results.

VAAST 3 includes the following enhancements:

  • Runs in under 10 minutes
  • Analyses intronic variants including splice regions
  • A single analysis report for indels and SNVs
  • Improved ranking results
  • Ensembl 75 annotations for background allele frequency database

 

A manuscript describing VAAST 3.0 is in preparation.

VAAST 2 will be supported through the end of 2015 to enable users to complete projects or studies that have already been initiated, and for validation purposes.

 


Reducing False Positives in Family Reports using Ref Call & No Call Data

VAAST Trio and Quad reports generated from vcf files containing Ref Call & No Call data will display open circles for ref calls, and dashes ("-") for no calls for the parents. For these reports, an additional "Filter False Positives" option will be available under the De Novo mode of inheritance. This option filters out any variants where both parents do not have a no ref call (both alleles).

 


Data Source & Algorithm Versions

 Opal Pipeline 5.0 - Released November 17, 2015

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinVar (downloaded November 2015)
  • COSMIC v71
  • dbNSFP version 2.9
  • dbSNP release 144
  • ENSEMBL version 75
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO October 28, 2015 15:00
  • GERP++ 2010 release
  • Genome Reference Consortium Human Genome Build v37
  • GWAS catalogue (downloaded May 21, 2014)
  • HGMD Public version 7.1
  • Human Phenotype Ontology build #98
  • Human Phenotype Ontology OBO 1698
  • MutationTaster (dbNSFP v2.9)
  • Omicia Score v2.0
  • OMIM (downloaded November 6, 2015)
  • PhastCons - phastCons46way (October 8, 2012)
  • PhenCode / LSDB (download April 30, 2014)
  • PolyPhen-2 v2.2.2 (dbNSFP v2.9)
  • SIFT (dbNSFP v2.9)
  • SiPhy v0.5
  • VAAST Variant Prioritizer v0.5

 

 

 

 

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